make_graph: make_graph

View source: R/steps.R

make_graphR Documentation

make_graph

Description

Make correlation or cooccurrence network

Usage

make_graph(
  ret,
  num_words = 30,
  cor_threshold = 0.2,
  cooccurrence = FALSE,
  whole = FALSE,
  bn = FALSE,
  R = 20
)

Arguments

ret

biotext class object

num_words

number of words to include

cor_threshold

correlation threshold

cooccurrence

use cooccurrence

whole

return correlation or cooccurrence for whole words

bn

perform Bayesian network inference

R

parameter for boot.strength function

Details

Make correlation or cooccurrence network based on biotext object. The resulting raw network is stored in 'igraphRaw' slot in biotext object. The networks can be customized in the subsequent functions like 'process_network_gene'.

Value

biotext class object

Examples

testgenes <- c("IRF3","PNKP","DDX41","ERCC1","ERCC2","XRCC1")
obtain_refseq(testgenes) |> 
make_corpus() |> make_TDM() |> make_graph()

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.